Contacts of the helix formed by residues 487 - 503 (chain B) in PDB entry 3GUT
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 487 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483B ASP* 5.7 2.5 - - - +
485B GLN 4.4 5.6 - - - +
486B LEU* 1.3 79.3 - - - +
488B ASP* 1.3 62.5 + - - +
489B ARG* 3.5 7.2 + - - +
490B GLU* 2.6 49.6 + - - +
491B LYS* 3.1 25.2 + - - +
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Residues in contact with ASP 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487B THR* 1.3 73.4 - - - +
489B ARG* 1.3 63.4 + - - +
490B GLU 3.2 2.0 - - - -
491B LYS* 3.4 27.5 + - - +
492B GLU* 3.4 25.3 + - - +
495B ARG* 5.0 1.0 + - - -
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Residues in contact with ARG 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475B TYR* 6.0 1.6 - - - -
487B THR* 3.5 6.4 + - - +
488B ASP* 1.3 76.5 - - - +
490B GLU* 1.3 66.2 + - + +
492B GLU* 3.6 23.6 - - - +
493B ILE* 3.3 39.0 + - - +
496B GLN* 4.4 11.3 - - - +
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Residues in contact with GLU 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473B LEU* 4.7 8.2 - - + +
475B TYR* 2.6 44.2 + - - +
476B LEU* 3.5 16.8 - - + +
483B ASP* 4.1 4.9 - - - +
485B GLN 4.1 1.0 - - - +
486B LEU* 3.1 22.9 - - + +
487B THR* 2.6 56.0 + - - +
488B ASP 3.2 0.2 - - - -
489B ARG* 1.3 80.2 - - + +
491B LYS* 1.3 61.3 + - - +
492B GLU 3.1 0.4 - - - -
493B ILE* 3.4 9.4 + - - +
494B ILE* 2.9 31.0 + - + +
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Residues in contact with LYS 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B LEU* 3.2 27.2 + - + -
487B THR 3.1 29.9 + - - +
488B ASP* 3.4 29.5 + - - +
489B ARG 3.3 0.6 - - - -
490B GLU* 1.3 77.0 - - - +
492B GLU* 1.3 58.7 + - - +
494B ILE* 3.4 9.9 - - - +
495B ARG* 3.0 52.9 + - - +
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Residues in contact with GLU 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488B ASP 3.4 15.0 + - - +
489B ARG* 3.6 25.8 - - - +
490B GLU 3.1 0.6 - - - -
491B LYS* 1.3 74.8 - - - +
493B ILE* 1.3 64.4 + - - +
494B ILE 3.1 1.3 - - - -
495B ARG* 2.5 45.9 + - - +
496B GLN* 3.0 38.5 + - - +
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Residues in contact with ILE 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469B VAL* 5.2 0.4 - - + -
470B HIS* 3.3 42.6 - - + +
472B ASP* 3.6 19.5 - - - +
473B LEU* 4.2 20.6 - - + -
489B ARG* 3.3 43.0 + - - +
490B GLU* 3.4 9.4 + - - +
492B GLU* 1.3 75.9 - - - +
494B ILE* 1.3 58.7 + - - +
496B GLN* 3.2 12.1 + - - +
497B ALA* 2.9 27.9 + - - +
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Residues in contact with ILE 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452B GLU* 3.9 24.0 - - + +
455B MET* 3.9 15.6 - - + +
456B THR* 3.7 22.7 - - - +
459B CYS* 3.7 24.0 - - + -
469B VAL* 3.6 24.5 - - + -
473B LEU* 3.8 6.5 - - + -
486B LEU* 4.7 6.5 - - + -
490B GLU* 2.9 22.9 - - + +
491B LYS* 3.4 11.9 - - - +
493B ILE* 1.3 77.5 - - - +
495B ARG* 1.3 56.7 - - - +
497B ALA* 3.1 5.9 + - - +
498B ALA* 2.9 31.8 + - - +
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Residues in contact with ARG 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B PHE* 4.5 5.5 - - + -
452B GLU* 2.9 31.9 - - - +
488B ASP 5.0 0.8 + - - -
491B LYS* 3.0 45.4 + - - +
492B GLU* 2.5 44.3 + - - +
494B ILE* 1.3 77.1 - - - +
496B GLN* 1.3 58.9 + - + +
498B ALA* 4.0 1.2 - - - +
499B VAL* 3.2 27.2 + - - +
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Residues in contact with GLN 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B ARG* 4.4 14.6 - - - +
492B GLU* 3.0 38.5 + - + +
493B ILE* 3.6 11.3 - - - +
495B ARG* 1.3 77.2 - - + +
497B ALA* 1.3 60.9 + - - +
499B VAL* 3.4 12.4 - - - +
500B GLN* 3.2 24.4 - - - +
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Residues in contact with ALA 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455B MET* 3.7 12.8 - - + -
469B VAL* 3.4 29.8 - - + +
470B HIS* 4.7 8.3 - - + +
493B ILE 2.9 15.7 + - - +
494B ILE 3.1 2.0 + - - +
496B GLN* 1.3 75.6 - - - +
498B ALA* 1.3 60.5 + - - +
500B GLN* 3.8 3.1 - - - +
501B GLN* 2.8 41.7 + - - +
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Residues in contact with ALA 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B PHE* 3.7 17.0 - - + -
451B LEU* 3.2 29.6 - - + +
452B GLU* 4.0 19.7 - - + +
455B MET* 4.0 1.0 - - - -
494B ILE 2.9 17.4 + - - +
495B ARG 4.0 2.9 - - - +
497B ALA* 1.3 77.3 - - - +
499B VAL* 1.3 54.4 + - - +
501B GLN 3.9 0.3 - - - -
502B THR* 2.7 38.4 + - - +
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Residues in contact with VAL 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B PHE* 3.3 21.0 - - + -
495B ARG 3.2 19.2 + - - +
496B GLN* 3.4 15.0 - - - +
498B ALA* 1.3 78.8 - - - +
500B GLN* 1.3 70.1 + - + +
502B THR* 3.0 14.6 + - - +
503B LYS* 3.8 10.4 + - - +
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Residues in contact with GLN 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496B GLN 3.2 19.4 - - - +
497B ALA* 3.4 5.3 + - - +
498B ALA 3.3 0.4 - - - -
499B VAL* 1.3 88.7 + - - +
501B GLN* 1.3 59.4 + - + +
503B LYS* 3.0 69.3 - - - +
504B GLU* 4.8 0.5 + - - +
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Residues in contact with GLN 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405B HIS* 3.1 54.0 + - + +
406B LEU 4.1 7.8 + - - +
451B LEU* 4.8 8.3 - - + +
455B MET* 3.3 21.8 - - - +
468B LEU 3.8 2.3 + - - +
469B VAL 3.2 25.7 + - - -
497B ALA* 2.8 21.7 + - - +
498B ALA* 4.1 3.1 - - - +
500B GLN* 1.3 76.6 - - + +
502B THR* 1.3 60.4 + - - +
503B LYS 3.3 2.5 - - - -
504B GLU* 3.6 19.7 + - - +
505B MET* 3.8 13.4 + - + +
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Residues in contact with THR 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B VAL* 3.9 21.1 - - + +
448B PHE* 3.6 37.8 - - + +
451B LEU* 4.4 11.2 - - + -
498B ALA 2.7 21.7 + - - +
499B VAL* 3.0 17.7 + - - +
501B GLN* 1.3 70.9 - - - +
503B LYS* 1.3 59.3 + - - +
504B GLU 3.0 6.5 + - - -
505B MET* 4.1 13.2 + - + +
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Residues in contact with LYS 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499B VAL 3.8 6.4 + - - +
500B GLN* 3.0 51.3 - - - +
502B THR* 1.3 80.7 + - - +
504B GLU* 1.3 84.2 + - + +
505B MET 4.0 0.2 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il